modules/fcs_fcsgx

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

assemblygenomicsquality controlcontaminationNCBI

https://github.com/nf-core/modules/[...]/modules/nf-core/fcs/fcsgx

Description

Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`assembly`
`:file`

assembly fasta file

`taxid`
`:string`

Taxonomic id (e.g. “6973”)

`gxdb`
`:file`

The NCBI GenBank database to search against.

Output

name:type

description

pattern

`fcs_gx_report`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`out/*.fcs_gx_report.txt`
`:file`

Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW)

*.fcs_gx_report.txt

`taxonomy_report`

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’ ]

`out/*.taxonomy.rpt`
`:file`

Report containing the contig identifier and mapped contaminant species

*.taxonomy.rpt

`versions_fcsadaptor`

`${task.process}`
`:string`

The name of the process

`fcsadaptor`
`:string`

The name of the tool

`0.4.0`
`:string`

The expression to obtain the version of the tool

`versions_python`

`${task.process}`
`:string`

The name of the process

`python`
`:string`

The name of the tool

`python3 --version |& sed 's/Python //'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`fcsadaptor`
`:string`

The name of the tool

`0.4.0`
`:string`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`python`
`:string`

The name of the tool

`python3 --version |& sed 's/Python //'`
`:eval`

The expression to obtain the version of the tool

Tools

fcs

"The Foreign Contamination Screening (FCS) tool rapidly detects contaminants from foreign organisms in genome assemblies to prepare your data for submission. Therefore, the submission process to NCBI is faster and fewer contaminated genomes are submitted. This reduces errors in analyses and conclusions, not just for the original data submitter but for all subsequent users of the assembly."

ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools github.com/ncbi/fcs/wiki/FCS-GX https://github.com/ncbi/fcs

modules/fcs_fcsgx

Description

Input

`meta`
`:map`

`assembly`
`:file`

`taxid`
`:string`

`gxdb`
`:file`

Output

`fcs_gx_report`

`meta`
`:map`

`out/*.fcs_gx_report.txt`
`:file`

`taxonomy_report`

`meta`
`:map`

`out/*.taxonomy.rpt`
`:file`

`versions_fcsadaptor`

`${task.process}`
`:string`

`fcsadaptor`
`:string`

`0.4.0`
`:string`

`versions_python`

`${task.process}`
`:string`

`python`
`:string`

`python3 --version |& sed 's/Python //'`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`fcsadaptor`
`:string`

`0.4.0`
`:string`

`${task.process}`
`:string`

`python`
`:string`

`python3 --version |& sed 's/Python //'`
`:eval`

Tools

fcs

maintainer

get in touch

modules/fcs_fcsgx

Description

Input

meta:map

assembly:file

taxid:string

gxdb:file

Output

fcs_gx_report

meta:map

out/*.fcs_gx_report.txt:file

taxonomy_report

meta:map

out/*.taxonomy.rpt:file

versions_fcsadaptor

${task.process}:string

fcsadaptor:string

0.4.0:string

versions_python

${task.process}:string

python:string

python3 --version |& sed 's/Python //':eval

Topics

versions

${task.process}:string

fcsadaptor:string

0.4.0:string

${task.process}:string

python:string

python3 --version |& sed 's/Python //':eval

Tools

fcs

maintainer

get in touch

`meta`
`:map`

`assembly`
`:file`

`taxid`
`:string`

`gxdb`
`:file`

`fcs_gx_report`

`meta`
`:map`

`out/*.fcs_gx_report.txt`
`:file`

`taxonomy_report`

`meta`
`:map`

`out/*.taxonomy.rpt`
`:file`

`versions_fcsadaptor`

`${task.process}`
`:string`

`fcsadaptor`
`:string`

`0.4.0`
`:string`

`versions_python`

`${task.process}`
`:string`

`python`
`:string`

`python3 --version |& sed 's/Python //'`
`:eval`

`versions`

`${task.process}`
`:string`

`fcsadaptor`
`:string`

`0.4.0`
`:string`

`${task.process}`
`:string`

`python`
`:string`

`python3 --version |& sed 's/Python //'`
`:eval`